On Mar 20, 2021, at 1:07, Fischl, Bruce <BFISCHL@MGH.HARVARD.EDU> wrote:

HI Mudathir

 

Looks like mri_vol2surf doesn’t want the full path in the “surf” parameter – just stuff after the “lh.”.

 

Cheers

Bruce

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of ????·????
Sent: Friday, March 19, 2021 2:21 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] equivolumetric surfaces

 

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Dear freesurfer experts,

 

I want to create an equivolumetric surfaces (using the tool from: MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/kwagstyl/surface_tools) and to sample the intensities of the T1wDividedByT2w volume at all the depths. I created the surfaces and after running the mri_vol2surf command I faced the error below. I don’t know why the path to the surface is not correct. I tried it in different devices with different versions of freesurfer but the results were the same. Any idea what I did wrong? Thanks

 

Mudathir

 

#################################################

-------- freesurfer-darwin-macOS-7.1.1-20200811-8b40551 --------
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME       /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR      /Applications/freesurfer/7.1.1/subjects
MNI_DIR           /Applications/freesurfer/7.1.1/mni
FSL_DIR           /usr/local/fsl
mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz --out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
srcvol = /Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target reference.
-------- original matrix -----------
 1.00000   0.00000   0.00000   0.00000;
 0.00000   0.00000   1.00000   0.00000;
 0.00000  -1.00000   0.00000   0.35001;
 0.00000   0.00000   0.00000   1.00000;
-------- original matrix -----------
Reading surface /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
error: No such file or directory
error: MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial): could not open file
error: No such file or directory
error: mri_vol2surf: could not read surface /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
mudathirbakhit%

#################################################

 

 

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